PROGRAM: DNA & Evolution
AUTHOR: Larry Massett
The non-chemist has a dog that kills possums.
Most dogs are bamboozled by the playing-dead routine. Not this dog. She knows the real thing when she sees it and she does want to see it, preferably with a severed head under the white lilac and a tail way over by the peonies and blood everywhere. That's dead.
So the non-chemist is crawling around the lawn on hands and knees stuffing scattered possum bits into a garbage bag, praying the neighbors won't notice, when suddenly...a crepitation at the back of the neck, the hair sprouting eyes to look behind. Who's watching?
It's a raccoon. Plump, calm, seated by the lilac. It has a mangled robin in its grip. The raccoon is watching with professional curiosity. Pausing now and again to nibble-a wing tip here, a sliver of breast there-it asks, one carnivore to another: is that how you do it, you humans? With garbage bags?
The non-chemist finds no way to dispute the complicity that is being assumed other than to stand up and declare, "You're mistaken. We are not One."
Inter-species conversation being what it is, the raccoon merely coughs.
The non-chemist is gratified to note the creature is dining on more feathers than will be good for it later on, poor thing-Procyon lotor, so far down the ladder of evolution. Glowing with bipedal, large-brained superiority, the human sweeps up the garbage bag and marches into the house; through the living room, through the dining room, the kitchen ("let's just have vegetables tonight, okay?"), and into the den, where a coffee table is stacked with books on genetics and evolution. These books are meant for a popular audience, and some of them resort to cartoons. They've been piling up for months anticipating a week at the beach. They're a hobby waiting to happen.
Now would be a good moment to look at them.
Pages rustle, hours pass. By the time the sun sets the non-chemist is beginning to think the raccoon may have a point. It seems that all life on earth is genetically related. Human genes are said to be 98 percent the same as a chimpanzee's, 70 percent the same as yeast, and-for goodness' sake-one book claims we're 30 percent the same as a day lily. Flower to fungus to biped, we're just variations on DNA, aren't we?
DNA is deoxyribonucleic acid. For once a tortuous chemical name appears to reflect a tortuous reality. The molecule is supposed to give out directions for making proteins, but on its own it can't do much. It requires the help of ribonucleic acid-RNA-to transfer information from the nucleus of the cell to the cytoplasm outside, where other micro particles called ribosomes set about actually assembling the proteins. This is the short version. On closer examination the operations are so complicated that the non-chemist is tempted to suspect it can't really happen.
It happens anyway. The non-chemist shrugs, but wonders how such a complicated way of doing business arose. Surely a good engineer could find a simpler method? Evidently DNA wasn't designed by the best minds at MIT. It must have come about through evolution.
Evolution...more rustling of pages as the moon rises over the lawn...evolution happens because mistakes happen when genes replicate. The mistakes are called mutations. Sexual reproduction brings changes too, by reshuffling the genes of the parents. Many of these changes make little difference. Once in a while, though, the novelty turns out to be an advantage. "Advantage" is defined as the chance one will live longer and pass on more offspring than one's neighbors. That all depends on the environment of the day. A thick coat of hair is a nuisance in the heat, but suppose an ice age comes along? Is it an advantage to have dark skin? Long legs? Perfect pitch? It depends. If circumstances are right the novelty will catch on.
But wait a minute: evolution as we know it is inseparable from DNA. To ask about the evolution of DNA is to ask about the evolution of evolution itself. How did evolution get started? Come to think of it, evolution-as-we-know-it looks to be inseparable from life-as-we-know-it. The non-chemist, who was only wondering why deoxyribonucleic acid is such a bear, now faces a Really Big Question. What's the origin of life?
A quick trot around the coffee table turns up no generally accepted definition of life. On the contrary, defining life appears to be a parlor game. It sounds like decent sport, late at night before an open fire. Jack makes up a checklist of all the attributes which Jack thinks are proper to "life." He may include-why not-the ability to reproduce. Jill makes up a different list. Hers-why not-omits reproduction. Common, she argues, but dispensable; angels don't bother with it. Jack says angels don't exist. Perhaps not, replies Jill. Yet suppose they did, or suppose they will one of these days; are you saying angels can't possibly exist or that if they did they wouldn't be alive?
The night wears on. This is getting nowhere.
This is why, eventually, the non-chemist next makes a trip to Yale University, to visit with Alan Weiner and his wife Nancy Maisels. Both teach molecular biophysics and biochemistry, and together they search for the origins of life. This is a specialty, Alan says, which scientists used to avoid like the plague because no one could think what to say about it. There were too few facts. He himself was nudged into the field by his Ph.D. advisor, James Watson ("Watson" as in "Watson - and - Crick - who - discovered - the - double - helix - and - whose - nudges - are - not - easily - ignored").
Alan: "Watson was writing a textbook and wanted a chapter on the origin of life. I thought I could write maybe ten pages on that. I would go home and try to convince Nancy this was interesting and she would try to convince me it was not."
Nancy: "For a while I thought evolution was the province of old men smoking pipes in paneled rooms. And then I realized that our cells are filled with records of our evolutionary past. You can almost do archeology looking at a contemporary cell. All of us really know lots of facts if we start thinking ... "
Alan: "We both became believers. One of the interesting things since then has been to watch our colleagues one by one come from saying no one can think about molecular evolution to being believers. One by one the disbelievers have come over...though there are a few stragglers left."
The non-chemist, before straggling to a belief in anything, would still like to know what "life" is.
Nancy: "I think life is something that's replicating itself in an informational way. So rocks aren't life, because you need something to make a rock, and then it's just a rock. A virus that can replicate itself is life."
Alan: "The essence of replication is that you can make interesting mistakes that will produce new molecules that are also capable of replication."
The non-chemist recalls that in recent years computers have been running programs that seem to replicate and evolve, at least in a mathematical or "informational" way. The prophets of artificial life claim that algorithms running off silicon chips can be as much alive as humans running off carbon molecules. Alan disagrees.
Alan: "At the risk of getting into trouble, that's foolishness. Because the other essence of life is that it takes place with the chemicals we have, and they constrain what you can do. You won't find a sculpture made out of pastels. It's determined by the chemicals on Earth today. If someone makes an equation that reproduces and mutates, that's not going to be life."
Nancy: "Most of us have a gut feeling about whether something's alive or not, and it doesn't take an education to know a computer's not alive."
Alan: "Hmm...what if the computer feels it's alive and we feel it's not?"
At this point the non-chemist is more than happy to abandon the parlor game. Assuming that life is...oh never mind...what everyone sort of feels it is...how did it start on Earth? To be sure, life might not have started on Earth, it might have dropped in from outer space. But wasn't there an experiment years ago in which researchers tried to recreate the atmosphere of the ancient earth in a test tube? And when they introduced electricity-a bolt of lightning, as it were-didn't some of the building blocks of life, like amino acids, form spontaneously?
Nancy: "I think a lot of people agree that lightning, fire, chemicals, amino acids: that's where the kind of life we're interested in got started."
Alan: "Chemists and biologists have very different views of the origins of life. For chemists the problem is to recreate that lightning situation, and they can't do it. So how would it have been possible in ancient times when there were no trained chemists? Biologists feel that since we have life today, we must be able to trace it back to earlier things, so they think it's the chemists' problem. Chemists look forward and get depressed, biologists look back and are excited."
Alan and Nancy, the non-chemist finally realizes, are not trying to work their way forward from a hypothetical moment of origin. They're looking at life as it is, hoping to work backwards. The clues are in the here-and-now.
Nancy: "Lots of biochemical reactions happen in straightforward ways and you can look at them and say, 'Oh, nature is beautiful or nature is logical.' And then some reactions happen in ways you would never have dreamed of, and you can either say, 'Well this is one of the times nobody was paying attention when they set it all up,' or you can think 'Maybe it's been this way for a long time and some of these molecules are doing this not because they're good at it but because they got stuck with the job long ago.'
"A friend of ours gives a wonderful analogy. His name's Gaby Dover and he says, 'Imagine that you get life up and running like an airplane in flight. And then you have to start fixing the airplane up. But you're not going to land it and convert the engine to a jet engine. What you're going to try to do is tinker.' And this is the evolution-as-a-grand-tinker-point of view. You've got something running and you can make changes as long as they don't cause the plane to crash. Some molecules are doing really important things and they can't stop doing them and give the job to somebody else. They're just going to be there forever. And those are the ones that are going to be in these mysterious reactions that you can look at and say, 'Oh, that's a clue.'"
The non-chemist discovers that Nancy and Alan share his naive opinion of DNA: the thing really is bizarre. This is the evolutionary clue, the hint that the airplane was re-designed in midair. Of special interest, they say, is the relation between DNA and RNA.
Nancy: "When you make DNA, when you make the nucleotides, the first thing you do is make RNA bases and then you turn them into DNA. Everybody thought this is bizarre. Well, if you believe that RNA evolved first, and DNA second, then the cell would have been set up to make the RNA and all it had to do was start this one extra reaction to make DNA later on. So you've taken a puzzle and turned it into something that not only is sensible, but explains something to us about our past."
Alan points out that RNA has a lot in common with DNA. It uses four molecules as a code to store information, three of these molecules being the same ones DNA uses. RNA can thus act as a genome, a storehouse of genetic information. Moreover, it can interact with other molecules in ways DNA can't. It can be a catalyst; it can make things happen all on its own. The more Alan and Nancy learn about the possibilities of RNA the more excited they get, because it looks to them as though some form of life could be carried on with only RNA.
Life doesn't need DNA?
The non-chemist is shocked. The molecular biochemists are thrilled, however. They are working up a vision of another world: a long-vanished microscopic world of life that could have flourished on Earth for billions of years before DNA ever appeared. They call it RNA World.
Nancy: "That's fairly stunning. To imagine that there was an equally complex but microscopic world out there that we have no fossil record of but we think we have the evidence for in contemporary molecules. If you look at RNA in our cells and viruses you get an idea of what used to be there."
Many of us agree there was a molecule something like the RNA that's in all of our cells today, and it was able to do two things: replicate itself and perform some basic chemical reactions. It was also serving as a kind of genome, the essence of information. Its functions have been taken over by DNA, which you hear so much about now, and by proteins.
Alan: "Most of us now think of DNA as a last-minute add-on, a more durable form of RNA. We don't see DNA as the master molecule."
Does the non-chemist detect a note of condescension toward DNA? Even a slight hostility? If the vision of RNA World is correct, then DNA may have been rigged up mainly as a sort of storage bin, a handy spot to park RNA's genomic information. And look what's happened: DNA stars in the textbooks, wins the Nobels, while RNA gets written up as a messenger, an errand-boy. It seems unfair.
Later, back at home sitting in front of an open fire, the non-chemist tries to image the ancient world of RNA. As usual, when contemplating microscopic existences, nothing springs to mind but a quivering image of little dots and a chuffing noise that suggests, for better or worse, a raccoon choking on a hairball. RNA World does not converse with humans. It is a mystery, though. RNA may have preceded DNA in evolution, but it's a complex molecule all the same. Where did it come from? When will we be tackling that question?
The fire dies out and the non-chemist recalls that most of the universe, perhaps 90 percent of it, is thought to be made of dark matter. This is a form of matter that can't be seen, let alone heard, touched, tasted, or smelled. The non-chemist once asked a cosmologist whether this dark world might contain stars and planets and-who knows-strange forms of life, advanced civilizations?
"Why not?" said the cosmologist.
From outside comes a squeal of tires, then a small thump. Then the sound of an engine accelerating again. A car has encountered a raccoon in the night, or else a possum. A certain quantity of genetic information will move to the dark side.
The non-chemist sighs, gets up to turn on the porch light, and wonders what electricity is.